Spatial Heterogeneity in Prey Availability, Feeding Success, and Dietary Selectivity for the Threatened Longfin Smelt

Food availability is a key determinant of the nursery value of a given habitat for larval and juvenile fishes. Growth, survival, and recruitment success are often inter-correlated and influenced by prey availability and associated feeding success. This is likely true for the threatened population of Longfin Smelt (Spirinchus thaleichthys) in the San Francisco Estuary (SFE) which has collapsed in recent decades along with its preferred prey. In years with high precipitation and freshwater outflow, larval Longfin Smelt are found in shallow wetland habitats throughout the SFE, but variation in the availability of food and feeding success in these habitats remains unexplored. To examine spatial variation in the trophic value of different rearing habitats, we quantified variation in prey availability, feeding success, and prey selection for larval and juvenile Longfin Smelt captured in restored tidal marshes, sloughs, and open-water habitats in the northern and southern SFE. Prey abundance varied spatially, with densities approximately tenfold greater in southern sloughs and restored tidal ponds relative to northern and open-water habitats. Feeding success of larval Longfin Smelt was positively correlated with both fish length and prey density. Larval Longfin Smelt fed selectively on the copepod Eurytemora affinis, with larger individuals (> 25 mm total length) exhibiting an ontogenetic diet shift to larger mysid shrimps. Our results suggest that wetland habitats across the SFE vary greatly in their trophic value, with previously unexplored habitats exhibiting the highest densities of prey and the highest foraging success for larval Longfin Smelt.

Assessing the distribution and abundance of larval Longfin Smelt: What can a larval monitoring program tell us about the distribution of a rare species?

Following its listing as threatened under the California Endangered Species Act in 2009, Longfin Smelt (Spirinchus thaleichthys) became a focus of resource managers in the San Francisco Estuary. Water exports were identified as one of the factors affecting Longfin Smelt abundance, and managers were challenged with balancing freshwater flows through the Sacramento-San Joaquin River Delta between human and ecosystem needs. This balance becomes especially challenging during the winter and spring when Longfin Smelt are spawning. Resource managers identified that the impact associated with entrainment of larval Longfin Smelt in the winter was uncertain, and to understand and manage this risk, new data was needed. In 2009 the Smelt Larva Survey was implemented and has since sampled newly hatched larvae from January–March. Here, I analyze this data and ask specific questions regarding distribution and densities of the larvae throughout five regions of the Upper Estuary – Napa River, Suisun, Confluence, Northern Delta, and Southern Delta – with the goal of understanding the spatial and temporal patterns of larval distribution since 2009. I found that larvae were most prevalent in the Suisun, Confluence, and Northern Delta regions, and less common in the Southern Delta and Napa River regions. Larval Longfin Smelt densities changed following a recent drought and record low population abundances. Median per-station averaged densities ranged from 154 to 274 fish per 1,000 m3 between 2009 and 2013 but declined to 1 to 65 fish per 1,000 m3 from 2014 to 2019. This survey data demonstrates that Longfin Smelt reproductive output has declined since their listing in 2009 and that their distribution into the Southern Delta is low relative to the rest of the Upper Estuary. These results reaffirm the species’ continued decline since its listing, and that improving the abundance of spawning adults is one of the many important steps needed for long-term recovery and resilience.

Genome-wide analysis reveals regional patterns of drift, structure, and gene flow in longfin smelt (Spirinchus thaleichthys) in the northeastern Pacific

The southernmost stock of longfin smelt (Spirinchus thaleichthys) is approaching extirpation in the San Francisco Estuary (SFE); however, patterns of genetic structure, diversity and gene flow which are vital for management are poorly understood in this species. Here, we use genome-wide data to evaluate population structure of longfin smelt across a broad latitudinal scale across estuaries ranging from the SFE to Yakutat Bay and Lake Washington, and fine scale within the Fraser River and the SFE. Results indicate high genetic structure between major estuaries, fine-scale structure within the Fraser River, and low levels of structure within the SFE. Genetic structure was more pronounced between northern estuaries whereas southern estuaries showed shared ancestry and ongoing gene flow, most notably unidirectional northward migration out of the SFE. Furthermore, we detected signatures of local adaptation within the Fraser River and the Skeena River estuaries. Taken together, our results identify broad patterns of genetic diversity in longfin smelt shaped by co-ancestry, unidirectional migration and local adaptation. Results also suggest that the SFE population is genetically distinct from northernmost populations and an important source for maintaining nearby populations.

Fewer and Farther between: Changes in the Timing of Longfin Smelt (Spirinchus thaleichthys) Movements in the San Francisco Estuary

Abundance of estuarine fish species has declined globally. In the San Francisco Estuary (SFE), long-term monitoring documented declines of many species including the anadromous species Longfin Smelt (Spirinchus thaleichthys). To improve management and recovery planning, we identified patterns in the timing, seasonal occupancy, and distribution of Longfin Smelt in a monitoring study (San Francisco Bay Study) for five regions of the SFE using a generalized additive model. We then investigated the year-to-year variability in the shape of the seasonal relationships using functional data analysis (FDA). FDA separated the variability due to population size from variability due to differences in occupancy timing. We found that Longfin Smelt have a consistent seasonal distribution pattern, that two trawl types were needed to accurately describe the pattern, and that the pattern is largely consistent with the hypothesized conceptual model. After accounting for variability in occupancy due to year-class strength, the timing of occupancy has shifted in three regions. The most variable period for the upstream regions Suisun Bay and Confluence was age-0 summer and for the downstream region Central Bay, was age-0 late fall. This manifested as a recent delay in the typical fall re-occupation of upstream regions, reducing Longfin Smelt abundance as calculated by another monitoring study (Fall Midwater Trawl); thus, a portion of recent reductions in Fall Midwater Trawl abundance of Longfin Smelt result from changes in behavior rather than a decline in abundance. The presence of multiple monitoring surveys allowed analysis of distribution from one data set to interpret patterns in abundance of another. Future investigations will examine environmental conditions as covariates during these periods and could improve our understanding of what conditions contribute to the shifting occupancy timing of Longfin Smelt, and possibly provide insight into the long-term quality of the San Francisco Estuary as habitat.

Feeding habits and novel prey of larval fishes in the northern San Francisco Estuary

Food limitation can dampen survival and growth of fish during early development. To investigate prey diversity important to the planktivorous larval longfin smelt (Spirinchus thaleichthys) and Pacific herring (Clupea pallasii) from the San Francisco Estuary, we used DNA metabarcoding analysis of the cytochrome oxidase I gene on the guts of these fishes and on environmental zooplankton samples. Differential abundance analysis suggested that both species consumed the most abundant zooplankton at a lower rate than their availability in the environment. Both fish consumed the prey that were commonly available and relatively abundant. Prey taxa substantially overlapped between the two species (Schoener’s index = 0.66), and alpha diversity analysis suggested high variability in the content of individual guts. Abundant prey taxa in both fish species included the copepods Eurytemora carolleeae, Acanthocyclops americanus, and A. robustus; the Acanthocyclops spp. are difficult to identify morphologically. A few uncommon prey in the diets hint at variable feeding strategies, such as herring (presumably egg) DNA in the longfin smelt diets, which suggests feeding near substrates. Herring consumed the small (<0.5 mm) copepod Limnoithona tetraspina more frequently (30%) than did smelt (2%), possibly indicating differences in foraging behavior or sensory abilities. Among the unexpected prey found in the diets was the cnidarian Hydra oligactis, the polychaete Dasybranchus sp., and a newly identified species Mesocyclops pehpeiensis. “Unknown” DNA was in 56% of longfin smelt diets and 57% of herring diets, and made up 17% and 21% of the relative read abundance in the two species, respectively. Our results suggest that these two fishes, which overlap in nursery habitat, also largely overlap in food resources necessary for larval survival.

Forage Fish Larvae Distribution and Habitat Use During Contrasting Years of Low and High Freshwater Flow in the San Francisco Estuary

Recruitment of estuarine organisms can vary dramatically from year to year with abiotic and biotic conditions. The San Francisco Estuary (California, USA) supports a dynamic ecosystem that receives freshwater flow from numerous tributaries that drain one of the largest watersheds in western North America. In this study, we examined distribution and habitat use of two forage fish larvae of management interest, Longfin Smelt Spirinchus thaleichthys and Pacific Herring Clupea pallasii, during a low-flow and a high-flow year to better understand how their rearing locations (region and habitat) may affect their annual recruitment variability. During the low-flow year, larval and post-larval Longfin Smelt were distributed landward, where suitable salinity overlapped with spawning habitats. During the high-flow year, larval Longfin Smelt were distributed seaward, with many collected in smaller tributaries and shallow habitats of San Francisco Bay. Local spawning and advection from seaward habitats were speculated to be the primary mechanisms that underlie larval Longfin Smelt distribution during the high-flow year. Larval Pacific Herring were more abundant seaward in both years, but a modest number of larvae were also found landward during the low-flow year. Larval Pacific Herring abundance was lower overall in the high-flow year, suggesting advection out of the area or poor recruitment. Future monitoring and conservation efforts for Longfin Smelt and Pacific Herring should recognize that potential mechanisms underlying their recruitment can vary broadly across the San Francisco Estuary in any given year, which suggests that monitoring and research of these two species expand accordingly with hydrologic conditions that are likely to affect their spawning and larval rearing distributions.